[gmx-users] simulate a substrate-bound enzyme

[Rui Li]

hello,everyone

I am new to gromacs. I am studing gromacs following the Tutorial for Drug -
Enzyme Complex,which was written by John E.Kerrigan,Ph.D. In the Tutorial, they
simulated a ligand-protein system, and they stripped the drug,parameterized it
using the PRODRG2 server. 

Now,I want to simulate a substrate-bound enzyme,and the drug has been bound with
enzyme(there is a bond between them). How can I parameterize the drug? If I
stripped the drug, how can I parameterize the bond between the drug and the
enzyme?